This contribution examines the natural philosophy underlying Avicenna's treatment of the basic physiological concepts of “innate heat”, “innate spirit”, and “radical moisture” in his famous Canon medicinae and the treatise De medicinis cordialibus appended to it in many Latin editions. Contrary to current belief, these concepts, far from being concisely systematized, fulfill a range of differing explicatory functions within the Canon and can only with great difficulty be harmonized into a unified theory. The paper analyzes these various concepts, based on a close reading of the relevant passages. It highlights, in particular, Avicenna’s corpuscular theory of matter, his insistence on the remarkable, ultimately occult powers of innate heat and many other things in nature, including even elementary fire, and his notion of colchodea, a celestial giver of the forms, which endowed inanimate and animate things with such powers. In conclusion, the paper suggests that the unparalleled, lasting popularity of the Canon in Western medicine may have been due not so much to the appreciation of its systematic account of the human body and its diseases but to the need of interpretation and commentary, which offered a welcome opportunity to academic physicians to show their learning and wit.